recipe bioconductor-hicbricks

Framework for Storing and Accessing Hi-C Data Through HDF Files

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/HiCBricks.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-hicbricks/meta.yaml

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

package bioconductor-hicbricks

versions:

1.18.0-0,  1.16.0-0,  1.11.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1, 

1.18.0-0,  1.16.0-0,  1.11.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rhdf5:

>=2.44.0,<2.45.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-curl:

depends r-data.table:

depends r-digest:

depends r-ggplot2:

depends r-jsonlite:

depends r-r.utils:

depends r-r6:

depends r-rcolorbrewer:

depends r-readr:

depends r-reshape2:

depends r-scales:

depends r-stringr:

depends r-tibble:

depends r-viridis:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-hicbricks

and update with::

   mamba update bioconductor-hicbricks

To create a new environment, run:

mamba create --name myenvname bioconductor-hicbricks

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-hicbricks:<tag>

(see `bioconductor-hicbricks/tags`_ for valid values for ``<tag>``)

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